I cannot say if this is your problem, but there is a known issue with some SKR pro boards. In fact the LED circuit is the source of the issue, and the LED can come on, but at the same time, the endstop not be registered by Marlin. The LEDs are pulling down the voltage so that the circuit no longer reads HIGH when the endstop is open. If this is your problem, your choices are:
- Get a replacement SKR Pro board
- Disconnect the endstop LEDs
- Add a pullup resistor between the ‘s’ pin and the ‘+’ pin for each endstop (or at least the one that is failing).
Adding a 1K or 1.5K pullup resistor can be done non-destructively, or you can solder them in like the image where you started to post before. Disconnecting the LEDs is a destructive operation.
Here is the topic where the issue was first explored and solutions proposed. There are several other topics on the forum concerning this issue.